Evidence map›Paper›PMID 30198894›Full record

ArticleActa crystallographica. Section D, Structural biology2018

New tools for the analysis and validation of cryo-EM maps and atomic models.

Pavel V Afonine, Bruno P Klaholz, Nigel W Moriarty, Billy K Poon, Oleg V Sobolev, Thomas C Terwilliger, Paul D Adams, Alexandre Urzhumtsev

Open access · hybridAbstract read
In one paragraph

Article in Acta crystallographica. Section D, Structural biology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 507 papers.

0numbers the graph read from it
0cells of the map it votes in
507citing papers in PubMed
60.5field-weighted citation impact, top 1% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

507 citing papers in PubMed, 841 citations in OpenAlex.

  1. Porcine serum maltase-glucoamylase: structure, kinetics, and inhibition.Journal of enzyme inhibition and medicinal chemistry · 2026
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  17. GαNature communications · 2026
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447 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors at 4 institutions in 3 countries.

Pavel V AfonineMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0002-5052-991X
Bruno P KlaholzCentre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS-INSERM-UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France.ORCID 0000-0001-8674-8674
Nigel W MoriartyMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0001-8857-9464
Billy K PoonMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0001-9633-6067
Oleg V SobolevMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0002-0623-3214
Thomas C TerwilligerBioscience Division, Los Alamos National Laboratory, Los Alamos, NM 87545, USA.ORCID 0000-0001-6384-0320
Paul D AdamsMolecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0001-9333-8219
Alexandre UrzhumtsevCentre for Integrative Biology, Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS-INSERM-UdS, 1 Rue Laurent Fries, BP 10142, 67404 Illkirch, France.
Lawrence Berkeley National Laboratory · USCentre National de la Recherche Scientifique · FRLos Alamos National Laboratory · USShanghai University · CN

Funding

PROJECT 5 - DUKE - STRUCTURE VALIDATION AND IMPROVEMENT FOR PROTEINS AND N. ACIDSP01GM063210 · NIGMS · UNIVERSITY OF CALIF-LAWRENC BERKELEY LAB · PI ADAMS, PAUL DAVID · 2001 to 2021
$33.5M
French Infrastructure for Integrated Structural Biology ANR-10-INSB-05-01National Institutes of Health GM063210NIGMS NIH HHS P01 GM063210U.S. Department of Energy DE-AC02-05CH11231
6 · The paper itself

Abstract

Recent advances in the field of electron cryomicroscopy (cryo-EM) have resulted in a rapidly increasing number of atomic models of biomacromolecules that have been solved using this technique and deposited in the Protein Data Bank and the Electron Microscopy Data Bank. Similar to macromolecular crystallography, validation tools for these models and maps are required. While some of these validation tools may be borrowed from crystallography, new methods specifically designed for cryo-EM validation are required. Here, new computational methods and tools implemented in PHENIX are discussed, including d

Indexed as

Models, MolecularSoftwareCryoelectron MicroscopyCrystallography, X-RayDatabases, ProteinHumansProtein ConformationProteinsProteinsatomic modelscryo-EMdata qualitymodel qualityresolutionvalidation

Identifiers

PMID30198894
PMCPMC6130467
OpenAlexW2791670278

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.